Simulation
by ChiaraStorm
Summary: Based on the Animatrix segment 'Program'. Cis and Duo had a history. And now it's all about to catch up with them.
1. Chapter I: Motionless

I had this story posted about six months ago, but I took it down because I didn't have time to work on it. Now though, I've made some improvements, and I hope that it's better. I'm not abandoning Awakening, never fear; I just wanted to branch out.

Thanks as always to the amazing **Bagpipes5K2** for all her help and support (hugs).

**Disclaimer: **I don't own anything of the Matrix franchise. If I did, do you really think I'd be writing fanfiction?

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**Chapter I: Memories**

Cis stood motionless in the elevator, hearing its familiar metallic grating and clinking as it ascended through the ship. She had closed her hazel eyes, revelling in the darkness beneath them. Even though the light of the ships was dim and unreliable, it still felt bright to her, painfully so. Darkness was good. It felt contemplative. It gave her a chance to think.

A white-hot flash of anger flared up inside of her. She could kill Kaiser. He was her brother, but that gave him no right to do that to her. She had gone into the Construct to kill time, to have fun. It almost ridiculous seemed to have fun whilst preparing for a war, but she had been fighting in this war for many years. Going into the Construct, loading up her favourite program was about as much fun as was possible around these ships.

The elevator pinged open, and light flooded into meet Cis' unprepared eyes. She squeezed them shut even tighter, and covered them with a hand as she gradually let them adjust to the light. She could practically sleepwalk from the lift to her room, having done it so many times before, but now it was different. She stumbled through the metal corridor, feeling as though she was drunk, a feeling she had experienced but once before in Zion. Mistakenly, she'd let her crewmate Echo order for her, and she'd woken up the next days with an aching head, painful eyes that couldn't bear light and a fuzzy, dazed feeling that she couldn't shake off for ages. This felt surprisingly like that, actually, except that she was thinking clearly. More clearly than she really wanted to be thinking. She'd like to just fall asleep and forget about it. However, she knew that she was too worked up and too emotional for that.

Padding along on silent feet, she almost slid into her room like a ghost. Cis lay down almost silently on the narrow bed, and stared at the ceiling with unseeing eyes. Thoughts were invading her brain like sentinels, and she made no effort to keep them out. If she could just deal with everything that had happened, then she would maybe get some sleep tonight.

Cis shivered suddenly. She was only wearing thin clothes, and they didn't cover all that much of her. It wasn't really her style, but she was training, and her real body would be sweaty and hot afterwards, even if it was only her RSI doing the work. Plus, if she got injured, it would be easier for a medic to heal her injuries. She didn't like it, but it was easier. She was usually fine after a training session. The ships were always cold, but you got used to it. Now, Cis was shivering like she had when she had first been unplugged. She curled up beneath the threadbare blanket, obviously recycled several times, and closed her eyes.

_Blood on her hands, on the ground, on her clothes…She could feel it, warm and sticky, almost heavy with the weight of its own importance. Liquid of life. It was everywhere. She hadn't expected so much. _

_She had her right shoulder up against his body, still warm, heart still beating. Her hands held up the broken-off blade, still through his throat, as if she was frozen that way. She could feel his body shudder with shock, and then stand absolutely still, the lack of movement more terrifying than if he was running at her with an axe. _

_The silver moon above her contrasted sharply with the immense crimson sky. The Oriental red, neither a stinging scarlet nor a subtle cherry, was almost multi-shaded, like tie-dye, or spilled blood. The blood running down her burnished sword and falling into her long, silvery hair exactly mirrored the sky and the moon. She could feel it, warm and fluid, running down her hair and warming her cool skin. _

_She was pressed into metal. Duo's armour was hardly soft or comforting, but it was his. It was familiar, almost more so than her own clothes. _

"_I wanted…to go back with you..." Cis stiffened as his words hit her in a hoarse, broken tone, unlike his usual smooth, serious voice. "I love you…"_

_His voice rolled through her like thunder. That same despair at his words, the same endless despair…_

Cis sat bolt upright, feeling a sense of déjà vu. She could sense that some time had passed by, but there was no way of knowing how long she had been dreaming for. It didn't really feel like a dream though. It felt almost like a trance, for it had been so vivid, so lifelike, that she was sure that it couldn't have just been a dream. She felt removed from time, stuck in a loop.

Brushing her hair out of her eyes, she sat back slowly and carefully. Her white hair, growing choppily around her face, had once been much longer, but about eighteen months ago, she had cut it herself, to keep it out of her face. She'd always loved having long hair, but it was too painful to keep it, after what had happened.

She ran her hands through it. The strands were a little matted with sweat and neglect; she didn't have time to take care of it. However, now it was even worse. There was something thick and tacky knotting the fine tresses. Something not unlike…

Cis got up, out of the bed, and headed towards a shelf where she kept toiletries and the like. Just soap and shampoo. Just little things she needed. Her hand went not to the small bronze bottles though, and headed instead for the small, round mirror she kept there. Holding it up, tilting it carefully, she searched through her hair, holding up strands and examining them carefully.

Nothing. The white strands were as pure and clean as ever. Just as she…

Cis froze mid-thought. There. The clump of hair she had just held up was still white, but striped with an ugly red streak, looking for all the world like it had been bleeding. Several other strands were stick to it, the sticky, scarlet gum that could only be blood.

Duo's blood. Duo's blood was matted in her hair. She could feel it on her fingers, cool and dry, clinging to her hair with determined force. It flaked on her fingers, almost like peeling an onion.

Cis blinked, hazel lights winking out and then returning in the briefest of motions. In that second though, the blood vanished.

She dropped the strand of hair like it was red-hot, and forced herself to take a couple of deep breaths. After she felt calmer, she ran her hand through her hair, searching each section carefully.

Nothing.

Her hair was snarled and tangled, as well as being far from clean, but it was free of blood. Cis ran her hands through it violently, tangling it even more than before, but convincing herself that there was no blood in it, least of all Duo's.

What had just happened?

She felt like she was back in the Matrix, not knowing the difference between being awake and being asleep. She felt vulnerable and ignorant, just like she had back then. A sudden memory hit her out of nowhere.

_Cis remembered the day it'd all started. It was almost a month after her brother, her older brother had gone missing without a trace. He'd taken nothing with him, everything in his room still complete. It was almost as though he'd simply walked down the street to see a friend, and would be back any moment. _

_But he wasn't coming back. He was gone. _

_Cis was devastated. He'd always been the stronger one, the more outgoing one, the one that always asked 'why?' Cis had always been the shy one, the one who had lingered in the shadows because she didn't know what to say. But despite these differences, he'd always looked after her, he'd been there for her. She knew he wouldn't have left without telling her. She just knew it, in her gut. _

_Cis had been sitting in his room after he left, looking on his computer. She knew he wouldn't leave without it. She used to tease him that his computer was his life, but after a while, the joke stopped being funny. The computer really was his life. She could sometimes hear him in the middle of the night, tapping away. He'd barely get any sleep, and he stopped talking to her. It was as though he really was living his life in a machine. _

_She'd found it then. Files and files, some downloaded legally, others taken from within a database thousands of miles away without their knowledge or consent. She'd found traces and programs and viruses and everything a hacker could use to dig a little deeper. She saw the websites he'd go onto, full of people asking each other the same question. _

_What is the Matrix? _

_So Cis had got involved. At first just to see if she could find her brother. But then, she had got caught up in it for its own sake, for the sheer beauty of destroying a system, of breaking the rules, and for the incredible need to find the answer. Not too long afterwards, she was contacted by a rebel, her now-captain, Styx. He'd brought some of his crew to meet her, and she'd been offered the red pill or the blue pill. She'd taken the red without hesitation. How could she turn his down? If she did, all she could look forward to was a life of regret and more questions. This way, she might at least get a few answers. _

_As she'd been freed, the first thing she heard in the real world was her Matrix name, being said over and over again. She was too weak to respond though, and it was only weeks later, once she was mobile and healthy, that she'd been able to find out who it was. _

_It was her brother. But not as she'd remembered him. He was Kaiser now. He'd been there, in the Matrix, as she went to meet Styx, but all dressed in black and his distinctive golden eyes obscured by opaque sunglasses, he'd been unrecognisable. And he couldn't say anything for fear that it would influence her decision on whether to take the red or blue pill. But now that she'd chosen, he could tell her. And in many ways, she was glad. She knew that he'd take good care of her. As always. _

_Kaiser had taken good care of her. But the person that had truly been there for her, through everything, had been another rebel, one freed long ago, yet he was still young. He'd been there with her through the training, and had answered her questions late at night, when curiosity kept her up as more and more questions grew. He'd been there for her. _

_Duo had been there for her…_

Cis sat up from the memory with a jolt, suddenly feeling like it was yesterday that she was unplugged instead of almost five years ago.

_Why now? Why do I still miss Duo so much? Why? Why can't I stop remembering him? Why do I feel like this? Why do I feel like crying right now? Why why why why why why…?_

Without warning, her long, tapered fingers clenched themselves into a fist which hurled itself against the metal wall. The impact didn't register with her – she barely felt it – but what struck her senses with jarring effect was the clunking, metallic echo of the hit. Cis could practically hear it rippling through the ship. She held her hand by the wrist, suddenly feeling like she was made of wet wool.

Her head was swimming. She didn't know why she'd done that. It seemed so masochistic, so unlike her. But in another way, it felt good. It reminded her of just how strong she really was.

So why was she breaking up over a little simulation?

"It wasn't real," she whispered to herself, her usually low and clear voice hoarse and cracking. "It wasn't real…" The words died on the air. She knew that they were a lie. Whether it was truly real or not was irrelevant. What really mattered was how it made her feel. And they made her feel ignorant, and guilty for trying to deceive herself.

_I don't care about the truth anymore…What's important is how we live our lives…_

Duo's words echoed in her head, and Cis felt even colder. Good. Let the cold claim her. She had once been so strong, so in control. Now she felt like a broken doll, thrown away, abandoned, neither wanted nor loved by anyone…

Cis shivered without warning. She was so tired, so very, very tired. She wanted nothing more than to sleep, sleep and forget everything.

"Duo…" she whispered slightly, curling up into a ball and huddling beneath the blankets, suddenly shivering and shaking uncontrollably. The warmth of her limbs, huddled up together beneath the worn blanket, was at once unbearable and not enough. She fell into a fitful sleep, tears of both regret and frustration drying next to each other on her cool cheeks.

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	2. Chapter II: Memories

**STUPIDHUMANZZ **– Wow! Thank you so much for saying that, I think now I've got a standard to live up to ;) Thanks for reviewing!

**Sydney Andrews – **Thanks! I agree, Animatrix characters are a lot harder to write, which is why I'm sure they're really out of character in this fic, but hey, it's artistic licence ;)

**Bagpipes5K2** – Yay! I love getting your reviews, they mean so much to me. Thanks for putting this on your favourites as well (hugs).

I meant to post this yesterday, but my grandmother broke her hip, so I was in and out of the hospital. I will have the next chapters up faster (I hope!), but I've got the start of my 22 exams next week, which won't end until June, so if I'm not updating, leave a comment at my LiveJournal (link in my profile) or email me and tell me to get a move on.

By the way, if any Awakening fans are about, I will have the next chapter up soon, it's just taking longer to write than I'd hoped. Sorry about that.

Enjoy!

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**Chapter II: Memories**

Duo opened his eyes, blinked once, and stretched out like a cat, long and full. Recently it had been harder than ever to get up. It wasn't that he was lazy or ill or anything like that.

It was because he could see Cis when he dreamed.

Probably why he enjoyed sleeping so much.

With a final stretch, he swung his legs over the side of the narrow bed, bringing himself into an upright position. He always stretched before he moved, as almost ten years of fighting and the subsequent injuries had left him stiff and inflexible first thing in the mornings. The coldness of the ship didn't help any either. In Zion they called it 'rebel's prediction', as it was meant to be a warning of things to come. The stiffness was only called that because it was pretty rare. Few people had been in the fight ten years or so.

He didn't know what they were meant to be doing today. He didn't really care. It was always the same stuff, always either repairing the ship, watching the code or jacking in to watch some new target or rather. It got so tedious, all the days ran together in an endless slipstream.

It had been different on the Hermes. It was more light-hearted – sure they were doing difficult and dangerous shit, but they were like a family. They all worked and played together. On this ship, he hadn't really wanted to get so involved again. It hadn't exactly worked out the first time…

Duo walked into the mess hall silently, a trick he had picked up over his years. Some of his crewmates, Alef and Sina, were sitting there, chatting quietly. Duo had never been able to join in properly, and they had given up trying to include him. They weren't cruel, but Duo had chosen his isolation. He hadn't even wanted to join this ship. He only did it for…

A word of Sina and Alef's conversation reached his ears, and he almost didn't believe what he was hearing. They couldn't have said that. They couldn't have known…

He wheeled around, moving so fast he made Alef visibly jump.

"Jeez, Duo, what's wrong with you?"

"What did you just say?" Duo demanded, his voice as soft and strong as before, but steely and hard. He knew Alef and

"I said 'Jeez, Duo, what's–"

"No, before that." Duo's dark face, sensitively lined with the intensity of his character, framed his blue-grey eyes, which were now clear and frozen with anger and confusion.

"I just said, are you still hung up about this?" Alef replied, indicating his food tray, his good-humoured face confused and frankly, a little weirded-out. Duo usually kept himself to himself. He wasn't exactly the type to get hung up because the food supply was running low and they were eating the stuff that was growing other stuff.

He breathed a sigh of relief. It wasn't anything about Cis. When he'd heard Alef asking him if he was still hung up about Cis, his heart had almost stopped. It wasn't that it was true or anything. It just surprised him. There wasn't any truth in it…

Oh, who was he kidding?

Was there anything wrong with missing Cis, the person who'd once been closer to him than his own shadow?

Yes. They'd left everything behind them a long time ago. He hadn't even seen her in ages – except in dreams.

It was when he had dreams like those he'd had last night. He'd never slept badly in the Matrix, until he started hacking, but really, at that point in his life he'd stayed up eighteen or nineteen hours a day, and sleep, when he had got it, had come easily. In the real world, at first, he'd been plagued with visions of those he'd killed – even though they weren't real, somewhere, in some mechanical power plant, someone had died because he shot a bullet in the virtual world. That sort of shit had haunted him, but he'd learned to live with it. He couldn't bear not to. It had been almost surgical, the cut between being a remorseful killer and being a killing machine.

He thought back to the dream. He didn't want to, but he had to.

He had been in a bamboo forest, like a Japanese ink painting. He could sense the simulation around him, the unreality of it all, and he knew who had written this program. He knew Cis always liked these sorts of programs. They reminded her of her childhood, growing up in Japan. Everything about the surroundings was clean and fluid, with an artistic streak which he knew could only belong to her.

The sky was calm, almost like snow hanging above his head. He could feel Cis' presence around him, serene yet poised for action.

There. He could see her, long white cape flapping in the wind and lifting her pale hair away from her face. Her skin was unnaturally white with traditional samurai paint, with the dots of red in the corner of each eye. Yes. He remembered it so well.

He called her name, loving the sound of it.

Cis turned, her silhouette framed against the sky. Her face was expressionless, but he thought he saw something flash in her hazel eyes, something that he recognised at first. Something like recognition. But there was something else there. Something he didn't expect.

At once they were much closer, a few metres away from each other as opposed to a ravine away. He could see the anxiety in her eyes, and the pulse in her neck flickering, almost in an erratic fashion. Panic – an unusual emotion for him – filled him up. He couldn't tear his eyes away from Cis. She seemed so distant, so remote right now. Others always thought she was like that, but never with Duo was she so far away. He got to see the side of her that no-one else got to see.

The silver sword flashed in the moonlight, a sudden streak through the darkness, and a sudden, almost clinical pain in his throat. He could feel Cis next to him, but he couldn't see her. His eyes were frozen in front of him, and all he could see was the weapon that was killing him.

He saw the shorn off end in a pair of white hands, and suddenly knew with a sickening realisation, that Cis was holding the blade.

Cis had killed him.

"Duo, man," Sina was looking at him intently, scrutinising him closely. "You okay?"

Duo's hands clenched into fists involuntarily. Something about Sina really grated his nerves, and he didn't know what it was. It almost seemed irrational, as he didn't really know any of the crew very well. He didn't want to know any of them very well. He was only on this ship, the Vishnu, because of Cis. He hadn't wanted to leave her, but it was too difficult for them to see each other every day, to be around each other after everything that had happened. To spare her sanity, he'd left. Simple as that.

No. There was nothing simple about it.

"I'm fine," he lied. He twisted lithely and walked out of the room as fast as possible, forgetting his hunger. He was hardly missing anything. The goop was enough to out anyone off of eating. Goop that was growing a new furry skin definitely put you off eating anything ever again.

He made his way, thankfully uninterrupted, back to his room. He would probably be needed up on the main deck, but he wouldn't be missed for a while. They knew where to find him anyway. There was no real privacy on these hulking metal giants. When he'd been on the Hermes, he hadn't minded so much. They were all so much closer. If he wanted to be alone for a bit, no-one would mind. If there was an emergency, he'd be there, just as anyone else would have been. But he could at least have some time to think.

_He remembered one time, after they'd jacked in. He'd immediately gone to his cabin, feigning tiredness, but just masking the real problem. _

_In the Matrix, he'd seen a date. 3rd November. Just a random date, but definitely not without significance for him. In the Matrix, he'd be celebrating however-many goddamn years of being alive. It was his birthday. _

_Surprisingly, he wasn't regretful, simply nostalgic. It was a rare moment of true reflection for him. He was so caught up in remembering the life, the part of him that didn't exist anymore he didn't hear the door open. _

"_Are you always alone like this?" _

_He looked up, and saw Cis, lingering in the doorway. Whilst her tone and pose were entirely casual, her eyes were completely serious, and there was a depth of concern that shocked him. _

"_Depends whether I want to be alone or not," he'd replied. _

_She smiled slightly. "Do you want to be alone now?" _

_He hadn't known what to say. He suddenly wanted her to stay, in his room, with him. Looking at her, he got the feeling that she knew what he was feeling so intensely that she wouldn't have wanted to leave, even if he asked her to. Duo found himself opening his mouth to ask her to stay, but the words wouldn't come. He couldn't find a string of words that would sum up everything he was feeling at that moment. So he just sat, and waited. _

_By the time he knew what to say, he was gone. _

Duo came back to reality with a thump, feeling out of control. He wasn't used to that. He was used to feeling free, as though he could do anything, but also as though he had a purpose. He wasn't usually so caught up with his thoughts, so introverted and reflective.

_If Cis met me now, would she recognise me? _

This thought was followed by a bitter laugh, echoing throughout his brain. He could almost taste the poison in the sound. His head was almost reeling with everything, a feeling that closely resembled what Cis had been feeling the night before, though he couldn't know that.

The memory crept into his mind, unbidden.

_He'd had a nightshift watching the Matrix. The code was difficult, and it was tiring for him to interpret, especially as it ran down almost too fast for him to read. By the end of his shift, he had a monster headache and he was pretty damn tired. He meant to walk back to his room and get as much sleep as possible, but he knew he wouldn't sleep with his headache, so he went to the mess hall to get some water. _

_When he'd entered, the harsh electric lighting had illuminated a solitary figure, exposing her to the world. Duo recognised Cis instantly, because even though her scalp was still covered in stubble, the pure white colour of it stood out, marking her. Having such distinctive colouring was not exactly helpful, for if a sentient program saw her, they wouldn't stint on sending in an Agent. It was beautiful though…_

_Cis sat up abruptly, her face paler than normal, and something not dissimilar to fear rolling over her face. Her eyes followed Duo as he moved around the room, going to the water tap. He didn't say anything, but as he turned around, he took in her features and expression, though no reaction showing on his face. _

"_Are you okay, Cis?" he asked finally, breaking the silence. _

"_Nothing – bad dream," she'd lied. He'd known it was something more. A little nightmare didn't make the whites of your eyes show. This was true fear, something stronger than your own will. _

_Duo said nothing, just sipped at his water, and watched her. The silence was oppressive, and she felt like she had to say something, just to break it. _

"_I just…" she began, her fists clenching as she struggled to find the words. _

_Duo watched, taking in the purpling bruise on her temple, and the streak of blood along the back of her hand, the skin around it raw, as though it had been grazed by a bullet…_

"_It was your first kill today, wasn't it?" he asked her, his low, rich voice kept quiet so that she could deny hearing it if she wanted to. _

_  
She didn't though. She met his eyes squarely, her clear hazel eyes reflecting the lights in the room. She seemed so vulnerable, so broken, yet there was a core of strength within her that didn't diminish. _

_Her hands were clenching so tightly he thought her nails were going to pierce her skin. Suddenly, without warning, the claws relaxed and she placed them over her eyes, covering up the clear pools of emotion. _

_She didn't let herself sob. She just needed to pretend to herself that she was away from him, that he couldn't see her._

_Cis knew he was there. And she didn't want to tell him. Her traitorous tongue however, moved before her brain kicked in. _

"_I pulled the trigger," she said softly, her voice slightly thicker than usual. "I watched him fall. It was so easy…" _

_She couldn't see, but she felt herself fitting easily into his arms. In fact, she didn't really know how it had happened. It just did. _

_Duo had no idea what had possessed him to hug her. There was so much he wanted to say, like he knew how she felt. Everyone did. Everyone had killed someone for the first time, and everyone had been traumatised by it, no matter how well they hid it. He wanted to tell her that she would be okay, not just because it got easier, but because he knew how strong she was. He'd watched her train, helped her spar, watched her as a crewmate and friend, and he knew just how strong she was. She would be okay. _

_He couldn't say any of that though, so he just hugged her. _

_She let herself hug him back, and he could feel her smaller frame beneath his. There, in that moment, had he first let himself realise it. Realise what was coming true…_

Duo came out of the memory with a bittersweet smile. Even though they stung, thinking about Cis, about the way things were, still kept him feeling human on the inside. It was so easy to become numb in this war, to forget what shred of humanity you had left. But Cis had helped him find his humanity.

But he couldn't forget his dream.

_Blood running down the sword, falling onto the stone. He knew he was dying. And his last thought, the last thing he would ever consciously think in this lifetime…_

_I'm so sorry, Cis…_

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